• Neuroscience

Systematic review protocol registration

This dataset contains neural recordings carried out from two different brain areas – dorsal Medial superior temporal cortex (MSTd) and ventral intraparietal cortex (VIP) – of eleven rhesus macaques. The data include recordings carried out using three different types of experiments: (1) Single-cell recordings during passive heading, (2) Single-cell recordings during active heading discrimination, and (3) Simultaneous recordings from pairs of neurons during passive heading. In each experiment, heading stimuli were delivered visually (optic flow) as well as vestibularly (platform). Experiment (2) contains an additional condition where we used a combination of visual and vestibular stimuli.

Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. The methods of cell transfection with electroporation can be found here: Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. Further explanation can be found here: Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499. Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10. This is IMAGE #2 (time point: 0 hours)of an image group. It is a second z-stack at this time point of a neuron from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. In the series, z-stacks of this neuron were acquired at a 2 hour interval for 8 hours. Afterward, a second time lapse series was acquired at a 60 second interval for 10 minutes. This time series shows dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions. The cell was transfected with in vivo electroporation of plasmid DNA encoding eGFP ~24 hours before the image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope Preparation: living tissue Relation to intact cell: whole mounted tissue Item type: recorded image Imaging mode: multi-photon microscopy Parameter imaged: fluorescence emission Source of contrast: distribution of a specific protein Visualization methods: EGFP Processing history: unprocessed raw data Data qualification: Raw;spatialmeasurements;intensitiesquantitation

Tongue traces and whistled frequency dataContains subdirected for each of the three whistled conditions. Each subdirectory contains a separate comma separate files for 1) F0 sampled from the audio, synchronized to MR data collection and downsampled to the same resolution so that each row corresponds to an MR image. Frames at which f0 could not be determined are marked --undefined-- and should be removed from both audio and MR data. 2) A vector Y coordinates beginning at the tongue root, 3) A vector a Z coordinates beginning at the tongue root.extracted_data.zipRaw rtMRI dataDicom format t1-weighted MRI images. Each .dcm file contains a single sagittal image that coresponds to one frame of MRI videography. Frames should be played a at a rate of 16.67Hz. Image headers were anonimised using MATLAB's dicomanaon function.raw_dicom.zipraw_dicom.zipPreprocessed audio.wav files cut to the length of each MRI scanning run. Files have been preprocessed to remove MRI noise artefacts. MB examined the files for remaining artefacts, clipping or breathy sections where f0 tracking was unreliable and forced the waveform to zero for such segments. For this analysis pipeline the effect is to remove MRI frames for that time period from further analysis.filtered_audio.zipvideoVideos of MRI data synchronized to preprocessed audio. Includes python code for constructing these videos from .dcm and .wav files.Belyk_whistle_fda_code1) Praat script for audio measurement. 2_Matlab script for tracing tongue masks. See github reference for previously release Matlab script for the creation of tongue masks. 3) R script for analysis pipeline including data import & wrangling, functional data analysis, and inference from linear mixed models.code.zip Most human communication is carried by modulations of the voice. However, a wide range of cultures has developed alternate forms of communication that make use of a whistled sound source. For example, whistling is used as a highly salient signal for capturing attention, can have iconic cultural meanings such as the cat-call, enact a formal code as in boatswain’s calls, or stand as a proxy for speech in whistled languages. We used real-time magnetic resonance imaging to examine the muscular control of whistling to describe a strong association between the shape of the tongue and the whistled frequency. This bioacoustic profile parallels the use of the tongue in vowel production. This is consistent with the role of whistled languages as proxies for spoken languages, in which one of the acoustical features of speech sounds are substituted with a frequency modulated whistle. Furthermore, previous evidence that non-human apes may be capable of learning to whistle from humans suggests that these animals may have similar sensorimotor abilities to those that are used to support speech in humans.

Software containers greatly facilitate the deployment and reproducibility of scientific data analyses in various platforms. However, container images often contain outdated or unnecessary software packages, which increases the number of security vulnerabilities in the images and widens the attack surface in the container host, and creates substantial security risks for computing infrastructures at large. This paper presents a vulnerability analysis of container images for scientific data analysis. We compare results obtained with four vulnerability scanners, focusing on the use case of neuroscience data analysis, and quantifying the effect of image update and minification on the number of vulnerabilities. We find that container images used for neuroscience data analysis contain hundreds of vulnerabilities, that software updates remove about two thirds of these vulnerabilities, and that removing unused packages is also effective. We conclude with recommendations on how to build container images with a reduced amount of vulnerabilities.

This dataset contains the distinct architectonic Area Ig2 (Insula) in the individual, single subject template of the MNI Colin 27 as well as the MNI ICBM 152 2009c nonlinear asymmetric reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of Düsseldorf. The results of the cytoarchitectonic analysis were then mapped to both reference spaces, where each voxel was assigned the probability to belong to Area Ig2 (Insula). The probability map of Area Ig2 (Insula) is provided in the NifTi format for each brain reference space and hemisphere. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and integration of new brain structures may lead to small deviations in earlier released datasets. Other available data versions of Area Ig2 (Insula): Kurth et al. (2018) [Data set, v11.0] [DOI: 10.25493/N7C7-BHW](https://doi.org/10.25493%2FN7C7-BHW) Kurth et al. (2019) [Data set, v13.1] [DOI: 10.25493/662G-E0W](https://doi.org/10.25493%2F662G-E0W) Kurth et al. (2020) [Data set, v14.0] [DOI: 10.25493/GSH9-K78](https://doi.org/10.25493%2FGSH9-K78) The most probable delineation of Area Ig2 (Insula) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D) Amunts et al. (2020) [Data set, v2.4] [DOI: 10.25493/A7Y0-NX9](https://doi.org/10.25493%2FA7Y0-NX9) Amunts et al. (2020) [Data set, v2.5] [DOI: 10.25493/8JKE-M53](https://doi.org/10.25493/8JKE-M53) Amunts et al. (2021) [Data set, v2.6] [DOI: 10.25493/KJQN-AM0](https://doi.org/10.25493%2FKJQN-AM0) Amunts et al. (2021) [Data set, v2.9] [DOI: 10.25493/VSMK-H94](https://doi.org/10.25493/VSMK-H94)

Specifications of the custom built two-photon microscope, including the laser sources, signal amplification, PMT specifications, and YFP filter sets are described in: Ruthazer ES, Li J, Cline HT. 2006. Stabilization of axon branch dynamics by synaptic maturation. J Neurosci 26(13):3594-3603. The methods of cell transfection with electroporation can be found here: Bestman JE, Ewald RC, Chiu S-L, Cline HT. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat Protocols 1(3):1267-1272. Further explanation can be found here: Bestman JE, Cline HT. 2008. The RNA binding protein CPEB regulates dendrite morphogenesis and neuronal circuit assembly in vivo. Proc Natl Acad Sci U S A 105(51):20494-20499. Bestman JE, Cline HT. 2009. The Relationship between Dendritic Branch Dynamics and CPEB-Labeled RNP Granules Captured in Vivo. Front Neural Circuits 3:10. This is IMAGE #4 (day 2) of a time lapse series contained with in this image group. It shows two neurons from the optic tectum of an albino Xenopus laevis tadpole CNS, stage 47. Autofluorescent pigment cells are visible in the superficial layers of the z-stack. The images were acquired daily over 2 days and show dendritic arbor development and morphological plasticity of the dendritic arbor with branch additions and retractions. The cell was transfected with in vivo electroporation of plasmid DNA encoding eYFP ~24 hours before the first image was acquired. The intact, living tadpole was anesthetized, positioned under a glass coverslip and this image was taken directly through its transparent skin using a custom built two-photon microscope. Preparation: living tissue Relation to intact cell: whole mounted tissue Item type: recorded image Imaging mode: multi-photon microscopy Parameter imaged: fluorescence emission Source of contrast: distribution of a specific protein Visualization methods: EYFP Processing history: unprocessed raw data Data qualification: Raw;spatialmeasurements;intensitiesquantitation

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